nf-core/jellyfish/count @ 0.0.0-0c7146d
Summary
Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm
Get started
Add the following snippet to your workflow script to include this module.
include { JELLYFISH_COUNT } from 'nf-core/jellyfish/count'
License
MIT License
Process
Name
|
JELLYFISH_COUNT |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
fasta
file
|
Nucleotide sequences in FASTA format *.{fasta,fa,fna,faa}
|
kmer_length
integer
|
k-mer size to use |
|---|
size
string
|
Specifies the memory hash size (in bytes) to allocate for the k-mer counting hash table (e.g., '100M'). A mean estimation could be carried with this formula: 'genome size + (genome size * coverage * kmer-length * error rate)' |
|---|
Output
2 channels
#1
jf
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.jf
file
|
Jellyfish binary k-mer database *.jf
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence | https://github.com/gmarcais/Jellyfish |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:50:13 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fjellyfish%2Fcount/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/jellyfish/count/blobs/sha256:aa4cbe90e65fcb9f6fb8dca7f2b494d2d9531a2a1f478db44ee7f31048108786 |
| Size | 2.5 KB |
| Checksum | sha256:aa4cbe90e65fcb9f6fb8dca7f2b494d2d9531a2a1f478db44ee7f31048108786 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:50:13 (UTC) | 1 | 2.5 KB | - |